A Belgian bishop has confessed to molesting a boy, becoming the first high-ranking prelate to be directly implicated in child sex abuse since the outbreak of the global scandal enveloping the Roman Catholic church.

Shortly after the Vatican announced that the pope had accepted his resignation , Roger Vangheluwe, the bishop of the Flemish city of Bruges, said that before he took over his diocese “and for a short time afterwards, I sexually abused a young boy close to me”.

In a letter read to a press conference, the 73-year-old prelate, who was not present, said what he had done more than 25 years ago “marked the victim forever”.

“The wound does not heal. Neither for me, nor for the victim,” he said.

Vangheluwe, who was consecrated a bishop in 1985, said he had several times begged for the forgiveness of the victim and his family – apparently to no avail.

His voice shaking with emotion, the head of the Belgian church and archbishop of Brussels, André-Joseph Léonard, acknowledged that the affair would have a painful effect on Belgian Catholics. “We are aware of the crisis of confidence that this is going to engender in a number of people,” he said.

Vangheluwe’s departure shattered the hopes of Vatican officials that the scandal could at last be contained. The affair had seemed to reach a turning point last weekend when, on a visit to Malta, Pope Benedict held a tearful meeting of reconciliation with abuse victims.

On Thursday, in an apparent confirmation of the Vatican’s new hard line, he accepted the resignation of James Moriarty, the bishop of Kildare and Leighlin in Ireland, who was accused in an official report of hushing up abuse cases. But yesterday the pope’s own past record was again called into question.

One of his cardinals said that before his election to the papacy, the pope had attended a meeting at which it was agreed to praise a French bishop for shielding a priest convicted of raping minors. In an interview in his native Colombia, Dario Castrillón Hoyos, who headed the Vatican department that deals with the clergy, said that a letter he wrote to the French bishop in 2001 was the product of a meeting in the Vatican.

“It was a meeting of cardinals. Therefore the current pope, who at that time was a cardinal, was present,” he said.

After the letter came to light, Castrillón said the last pope, John Paul II, had approved it and recommended that it be circulated – as it was – to all Catholic bishops. “The law in nations with a well-developed judiciary does not force anyone to testify against a child, a father, against other people close to the suspect,” Castrillón told his interviewer. “Why would they ask that of the church?”

His view was at odds with Vatican guidelines published last week, which make clear that bishops are expected to report clerical sex abuse to the authorities if required to do so by law. Church officials say the guidelines have been in force since 2003 – two years after John Paul II ordered that all such cases should be handled by the congregation for the doctrine of the faith, the department headed by his successor, the then Cardinal Joseph Ratzinger.

In a series of legal actions concerning abuse that dates from before then, the Vatican’s representatives have argued that the responsibility lies solely with the relevant diocese. But a new suit filed in the United States seeks for the first time to pin the blame on the Vatican, claiming that it exercises “unqualified power” over the Catholic church down to the level of its parishes.

The suit was filed on Thursday by Jeff Anderson, an attorney in St Paul, Minnesota. He argues that top officials in the Vatican, including Ratzinger, knew about claims of sex abuse at a school for deaf children near Milwaukee, and that they blocked the punishment of the accused priest, Lawrence Murphy.

Murphy, who died in 1998, is accused of molesting up to 200 boys between 1950 and 1974. The defendants in the lawsuit are the pope, Cardinal Tarcisio Bertone, who was his deputy at the congregation for the doctrine of the faith and is now his top official, and Cardinal Angelo Sodano, Bertone’s predecessor.

Some of the most damning evidence of systematic child abuse by the Roman Catholic clergy to come to light was unveiled today by Belgium’s leading authority on paedophilia, who published hundreds of pages of harrowing victim testimony detailing their traumas and suffering.

The explosive report by Peter Adriaenssens in the town of Louvain, east of Brussels, lists evidence of 476 instances of child abuse by priests and bishops going back 50 years.

Adriaenssens was appointed by the church last year to head an independent inquiry into the scandal. Since April, when Roger Vangheluwe, the bishop of Bruges, resigned after admitting persistently molesting a nephew, the Adriaenssens commission has been inundated with evidence, with hundreds of victims coming forward.

He has since documented cases of abuse occurring in almost every diocese in the country and in virtually every school run by the church. “We can say that no part of the country escapes sexual abuse of minors by one or several [church] members,” said Adriaenssens.

“This is the church’s Dutroux dossier,” he added in reference to the notorious Belgian paedophile serial killer, Marc Dutroux, who kidnapped, tortured, abused and murdered six girls in 1995-6.

Speaking of the victims, Adriaenssens said that 13 had killed themselves, according to relatives, and another six had attempted suicide.

The 200-page report includes copious anonymous testimony from 124 of the victims “to honour their courage” in coming forward.

“There are days when I thank God for having the chance to speak,” testified one woman.

“Four years of psychotherapy have taught me that silence kills. I have had enormous depressions, going as far as attempted suicide. At other times I think it would be wise to let sleeping dogs lie. But in the end I’ve chosen to speak … Since the resignation of the bishop of Bruges, I am living again in anxiety and fear. And I am far away. I’ve chosen to live far from my country, hoping that the past won’t rejoin me.”

This testimony was from a woman abused in the 1980s, but most of the cases concerned young boys and teenagers, as well a documented case of a two-year-old boy being molested.

Another victim told of being repeatedly sexually molested by his parish priest for five years from the age of seven.

“From being a violated child, I myself became, several years later, an abuser of adolescents and was sentenced to eight years in jail of which I served four and a half … The priest’s violations certainly strongly shaped my sexual identity and influenced my life choices.”

The evidence presented, said the daily newspaper Le Soir, was of “immense persistent suffering which neither the church, justice, nor society have been able to assuage … Adriaenssens has done what everyone else declined to do – listen to the victims, understand them, and give them the place they deserve.”

The abuse went back to the 1950s, was most common in the 60s and was tailing off by the 1980s, Adriaenssens said.

“The exposed cases are old, of course,” he said. “Society has developed. But there’s nothing to indicate that the number of paedophiles has diminished. Where are they today?”

Most of the victims were now middle-aged, but remained traumatised. Around half of the abusers had died.

The expert unveiled his report today because yesterday a Belgian court ruled that the material, seized by police in a highly controversial raid in June, was inadmissible in court because of the “disproportionate” police action and ordered it returned.

Pope Benedict criticised the Belgian authorities for “deplorable” conduct when in June they seized the commission’s files, raided the headquarters of the Belgian Catholic church, held cardinals and bishops for several hours, took their mobile phones, and carried away computers and documents.

They questioned Cardinal Godfried Danneels, who retired as head of the Belgian church and archbishop of Brussels in January.

Two weeks ago Belgian newspapers published tape recordings of Danneels seeking to hush up the case of Vangheluwe, the Bruges bishop.

Vangheluwe’s nephew secretly recorded Danneels pressing him to keep quiet about his uncle at least until he retired next year.

“I don’t think you’d do yourself or him a favour by shouting this from the rooftops,” the cardinal warned the victim, who replied angrily that his uncle had abused him for 13 years from the age of five.

The recordings were made in April and the bishop resigned two weeks later, the most senior clergyman in the Catholic church to have quit after being exposed for child abuse.